1/23 WHY WE ARE BUILDING AN OPEN PLAYBOOK FOR DEPLOYING GENOMIC PATHOGEN SURVEILLANCE.

Primarily for developing countries, but smaller towns in developed countries would also find this useful.
2/ I cover the WHY and WHY NOW of genomic pathogen surveillance in this other thread. https://twitter.com/kcorazo/status/1258698778606858240">https://twitter.com/kcorazo/s...
3/ In this thread, I& #39;d like to focus why the need now is scaling deployment—PROJECT MANAGEMENT:

https://abs.twimg.com/emoji/v2/... draggable="false" alt="✅" title="White heavy check mark" aria-label="Emoji: White heavy check mark"> Enabling technology has matured a lot: @nanopore

https://abs.twimg.com/emoji/v2/... draggable="false" alt="✅" title="White heavy check mark" aria-label="Emoji: White heavy check mark"> Scientists have repeatedly shown its feasibility https://scrapbox.io/kahlil/lab-in-suitcase_papers

https://scrapbox.io/kahlil/la... class="Emoji" style="height:16px;" src=" https://abs.twimg.com/emoji/v2/... draggable="false" alt="❓" title="Red question mark ornament" aria-label="Emoji: Red question mark ornament">Deployment playbook
4/ Let me do a quick review of the state of technology innovation, and lab-in-suitcase papers, then I& #39;ll show what a deployment playbook looks like.
5/ It seems the biggest **technology** challenge right now are reagents: prices, logistics and stability in tropical climates.

I wonder if projects like this will eventually fix this issue: https://app.jogl.io/project/174/ ">https://app.jogl.io/project/1... @Eyesgack https://twitter.com/arwynedwards/status/1259101958813691909">https://twitter.com/arwynedwa...
6/ Other innovations continue to lower costs. For instance, multiplexing, which allows multiple samples to be sequenced in a run, is increasing in capacity, thus lowering cost per sample https://nanoporetech.com/resource-centre/nanopore-sequencing-sars-cov-2-genome-introduction-protocol">https://nanoporetech.com/resource-...
7/ In the software side, "adaptive sampling". The sequencer can release the nucleic acid being read, based on real-time comparison w reference genomes. Flowcells are expensive, and this would increase their capacity by lessening reads of unwanted sections. https://twitter.com/mattloose/status/1224350276083240960">https://twitter.com/mattloose...
8/ @kirstynbrunker et al recently updated their paper. https://wellcomeopenresearch.org/articles/5-3 ">https://wellcomeopenresearch.org/articles/... With "nuclease-flush", which allows multiple runs per flowcell, they estimate the cost per sample to drop to ~£35 to £45. https://twitter.com/kcorazo/status/1258698830666543105">https://twitter.com/kcorazo/s...
9/ [[ @laura_boykin]] et al estimate that with the Flongle, cost could go down to as low as 4 USD https://www.mdpi.com/2073-4425/10/9/632/htm">https://www.mdpi.com/2073-4425...
10/ [[ @waywardsyintist]] - who used nanopore to for arbovirus genomic surveillance in the field https://www.nature.com/articles/s41598-018-23641-7">https://www.nature.com/articles/... - has started a company to provide a lab-in-suitcase solution based on that experience. My guess is that there will be more to come. https://twitter.com/waywardsyintist/status/1251238460796612608">https://twitter.com/waywardsy...
11/ [[Ahmed Abd El Wahed]]& #39;s suitcase lab is EUR8,000 excluding the laptop https://nanoporetech.com/resource-centre/nanopore-sequencing-missing-puzzle-piece-molecular-identification">https://nanoporetech.com/resource-... https://twitter.com/kcorazo/status/1258698836584759298">https://twitter.com/kcorazo/s...
12/ This list from [[ @NetworkArtic]] for sequencing Ebola gives us an idea
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Reagents: £6,890
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Equipment: £6,890
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Consumables: £887
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Cold Chain, Power, Storage: £2,686
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Grand total: **£17353**
https://artic.network/ebov/ebov-seq-kit.html">https://artic.network/ebov/ebov...
13/ The tech is ready and it is affordable. Scientists have shown feasibility. But how come developing countries are very slow in producing SARS-CoV-2 genomes? https://twitter.com/laura_boykin/status/1264922619813351424">https://twitter.com/laura_boy...
14/ The article linked to by [[ @laura_boykin]] above gives some answers.
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">They have the equipment and training.

https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">But there is lack of collaboration (eg, sampling org to sequencing org).

https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Gov& #39;t employee mindset: needs top-down orders to change work direction
15/ cont.
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond"> Lack of funding from govt (I suppose this is for reagents and other consumables considering they have equipment and training)

(prior to reading this, I assumed the biggest problems were lack of trained personnel and logistics of bringing in reagents)
16/ These sound to me like project management problems.
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Aligning work to what& #39;s needed to accomplish the project
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Working through the politics of organizations
https://abs.twimg.com/emoji/v2/... draggable="false" alt="🔹" title="Small blue diamond" aria-label="Emoji: Small blue diamond">Ultimately, being the single point of responsibility for getting the project done, on-time, on-scope and on-budget
17/ Given new low-cost alternatives to sequencing, why even work with large bureaucracies? What& #39;s stopping university labs, private labs and local government units from doing the sequencing themselves? Am I naive to think that this is simply a matter of execution?
18/ What does execution—the deployment of genomic pathogen surveillance—actually mean? There& #39;s actually an answer to that, just like there& #39;s an answer to "what& #39;s the right way to do accounting?" GAAP for the latter; PMBOK for the former https://en.wikipedia.org/wiki/Project_Management_Body_of_Knowledge">https://en.wikipedia.org/wiki/Proj...
19/ So how would a project management playbook for deploying genomic surveillance look like? Here& #39;s what a professional project manager would look for or create. https://scrapbox.io/kahlil/Resources:_Open_Playbook_for_Deploying_Genomic_Surveillance">https://scrapbox.io/kahlil/Re...
20/ A deployment in one location would be very similar to another one, so why not reuse these project planning and execution tools? Just include some project management training for first-time PMs.

This is essentially our JOGL project https://app.jogl.io/project/285 ">https://app.jogl.io/project/2...
21/ To get an idea of what these project management tools are, please check this other thread https://twitter.com/kcorazo/status/1266227623958507520">https://twitter.com/kcorazo/s...
22/ The urgent need is to provide richer SARS-CoV2 data for each locality. But it goes beyond COVID. According to the WHO, rabies kills 59,000 people/yr. In this map of arboviruses (eg, Dengue, Zika), we see that the worst hit is the developing world. https://www.sciencedirect.com/science/article/pii/S1201971217303089">https://www.sciencedirect.com/science/a...
23/23 Most of the work is PM, which me and @akinnaija could handle. However, subject matter experts in lib prep and bioinformatics would be helpful: just be in our Slack channel to see that we are not doing anything stupid & to answer occasional technical questions. Pls DM me!https://abs.twimg.com/emoji/v2/... draggable="false" alt="🙏" title="Folded hands" aria-label="Emoji: Folded hands">
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